Jardim et al. (2023): Supporting Information

Appendix S1

Author

Victor L. Jardim

This document contains all data analyses presented in the main text as well as supporting information mentioned and extra information on the analysis for those interested (not cross-referenced).

The analysis was organized using the make-line pipeline tool provided by targets (Landau 2021). You will find raw data as well as all functions used in the pipeline in the project’s research compendium created with the rcompendium package (Casajus N. 2022).

You can take a look at the pipeline in order to have an idea of the different steps for creating the main models and figures. Each target is defined at the _targets.R file in the research compendium.

 

 

 

Analysis pipeline. Total runtime and storage size of each object (target) are shown.

 

Table of figures

Supporting Main text
Figure S 1 Figure 1
Figure S 2 Figure 2
Figure S 3 Figure 3
Figure S 4 Figure 4
Figure S 5 Figure 5
Figure S 6 Figure 6
Figure S 7 Figure 7
Figure S 9 Figure 8
Figure S 8

Table of tables

Unfortunately links only redirect to tabsets open by default but not hidden ones. Please look for tables related to analyses by phylum or by compartment in their respective tabsets.

Supporting Tables
Table S 1
Table S 2
Table S 3
Table S 4
Table S 6
Table S 7
Table S 8
Table S 9
Table S 10
Table S 11
Table S 12
Table S 13
Table S 14

Packages

Code 
library(dplyr)
library(tidyr)
library(vegan)
library(ggplot2)
library(targets)
library(ggrepel)
library(patchwork)
theme_set(theme_light())

Habitat Complexity

Take a look at the structure of the final complexity dataset

Code 
tar_load(comp)
knitr::kable(head(comp))

 

First lines of the complexity dataset
Mini Site Point Sample Branching_density Broken_density D_bin D_gray L I S Total_Density Dry_weight Sphericity DR1 DR2 DR3
MBE_1 Belle-ile Belle-ile 1 1 5.8 0.0 1.1231 2.6562 12.85333 9.143333 8.303333 181696 183.61 0.8371338 0.6460062 0.8153846 0.7113589
MBE_1 Belle-ile Belle-ile 1 2 1.0 0.0 1.0654 2.6463 16.07667 7.883333 5.393333 181696 183.61 0.6122605 0.3354758 0.7669267 0.4903587
MBE_1 Belle-ile Belle-ile 1 3 3.0 0.2 1.0722 2.6450 15.30000 8.103333 7.190000 181696 183.61 0.7470808 0.4699346 0.8873818 0.5296296
MBE_1 Belle-ile Belle-ile 1 4 4.8 0.4 1.1078 2.6492 12.91667 8.476667 6.203333 181696 183.61 0.7057078 0.4802581 0.6613704 0.6562581
MBE_1 Belle-ile Belle-ile 1 5 4.2 0.0 1.1305 2.7019 24.54667 14.523333 8.970000 181696 183.61 0.6088477 0.3654264 0.6434838 0.5916621
MBE_1 Belle-ile Belle-ile 1 6 3.0 0.4 1.1198 2.6641 16.35667 9.416667 6.783333 181696 183.61 0.6684949 0.4147137 0.7249304 0.5757082

 

Most variables are not normally distributed so we apply a box-cox (Box and Cox 1964) transformation and check correlations between the transformed variables

Code 
tar_read(pairscomp)

Correlogram of box-cox transformed HC variables

PCA of all observations

Let’s check it without removing highly correlated variables

Code 
tar_load(pcatotal)
tar_read(sptot)

Screeplot of the PCA including all observations and all variables

We had up to 6 relevant axes to look at, but we know we have several highly correlated variables

Code 
tar_read(pcatot)

PCA of all observations and all variables
Code 
tar_read(pcatotsel)
Call: rda(X = num_sel, scale = TRUE)

              Inertia Rank
Total               5     
Unconstrained       5    5
Inertia is correlations 

Eigenvalues for unconstrained axes:
   PC1    PC2    PC3    PC4    PC5 
1.6866 1.1941 0.8642 0.6783 0.5768
Code 
tar_read(sptotsel)

Screeplot of the PCA including all observations and selected variables

Let’s check the biplots of the selected variables

Code 
tar_read(pcasel)

Supporting Figure 1: PCA of all observations after variable selection

PCA of median values

Code 
tar_read(spmedsel)

Screeplot of the PCA of median values at the point level

Let’s check the biplots of the selected variables

Figure 1  

Code 
tar_read(pcamed)

Figure 1 (main text)

Cluster of median site values

Let’s check if we find similar groupings using a ward’s cluster

Code 
tar_read(clustcomp)

Supporting Figure 2: Ward’s cluster of median complexity values at the site level

Correlation between the centroids of the total PCA and the scores of the reduced PCA

Code 
tar_load(corcomp)
plot(corcomp[[1]])
plot(corcomp[[2]])
tar_read(cortestcomp1)
tar_read(cortestcomp2)

    Pearson's product-moment correlation

data:  med_sel2$PC1_c and med_sel2$PC1_score
t = -16.404, df = 28, p-value = 6.824e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 -0.9769962 -0.9000432
sample estimates:
       cor 
-0.9517122 

    Pearson's product-moment correlation

data:  med_sel2$PC2_c and med_sel2$PC2_score
t = 25.364, df = 28, p-value < 2.2e-16
alternative hypothesis: true correlation is not equal to 0
95 percent confidence interval:
 0.9557115 0.9900324
sample estimates:
     cor 
0.978924

(a) PC1

(b) PC2

Supporting Figure 3: Relation between Full PCA centroids and Reduced PCA scores

Macrofauna data availabity

Code 
tar_load(faunadata)
knitr::kable(head(faunadata))

 

First lines of the original macrofaunal data
Point Site Replicate Method Habitat Year Season Date Species Abundance
Belle-ile 1 Belle-ile 1 Grab Maerl 2007 Spring 2007-03-11 00:00:00 Abludomelita gladiosa 1
Belle-ile 1 Belle-ile 1 Grab Maerl 2007 Spring 2007-03-11 00:00:00 Abra alba 1
Belle-ile 1 Belle-ile 1 Grab Maerl 2007 Spring 2007-03-11 00:00:00 Ampharete spp. 1
Belle-ile 1 Belle-ile 1 Grab Maerl 2007 Spring 2007-03-11 00:00:00 Amphipholis squamata 2
Belle-ile 1 Belle-ile 1 Grab Maerl 2007 Spring 2007-03-11 00:00:00 Anapagurus hyndmanni 1
Belle-ile 1 Belle-ile 1 Grab Maerl 2007 Spring 2007-03-11 00:00:00 Aonides oxycephala 3

 

Code 
samplespoint <- faunadata %>% 
  mutate(Date=as.factor(format.Date(faunadata$Date,"%Y"))) %>% 
  distinct(Site, Year, Point, Replicate) %>%
  group_by(Site, Year, Point) %>%
  mutate(Year = as.factor(Year)) %>% 
  summarise(count = n()) %>%
  ungroup() %>%
  mutate(State = factor(case_when(count==3 ~ "Good", count < 3 ~ "Sample(s) missing", count > 3 ~ "Too many samples")))

ggplot(samplespoint, aes(x=Year,y=Point,fill=State)) +
  geom_tile(alpha=0.5) +
  scale_fill_manual(values=c("palegreen3","lightblue", "indianred")) +
  geom_text(aes(label=count)) +
  theme(text=element_text(size =15), axis.text.x = element_text(angle = 90, size = 15), legend.position = "bottom")

Supporting Figure 4: Number of grab samples taken every year at each point. Empty cells show points where no samples were collected at a given date due to field constraints.

Local macrofaunal diversity

Total richness

Code 
# Total richness
tar_load(faunaclass)
total_rich <- nrow(faunaclass %>% 
  distinct(., Species)) #725 species

# Total richness by sediment position

epi_rich <- nrow(faunaclass %>% 
  filter(Position == "Epifauna") %>% 
  distinct(., Species)) #341 epifaunal species


inf_rich <- nrow(faunaclass %>% 
  filter(Position == "Infauna") %>% 
  distinct(., Species)) #266  infaunal species


int_rich <- nrow(faunaclass %>% 
  filter(Position == "Interstice") %>% 
  distinct(., Species)) #118 interstitial species

There are 725 species in total, 341 being epifaunal, 266 being infaunal, and 118 interstitial.

Relative abundance

Code 
tar_read(relab_phy)
tar_read(relab_ord)

(a) Main Phylla

(b) Main Orders

Supporting Figure 5: Average Relative Abundance of Main Phyla and Orders

p.s.: it is normal to have NAs for some orders as higher classification for some of the species is ambiguous or unknown.

Code 
tar_read(relab_arth)
tar_read(relab_ann) 
tar_read(relab_mol)

(a) Arthropoda

(b) Annelida

 

(c) Mollusca

 

Supporting Figure 6: Families Average Relative Abundance for Each Main Phyla

Effects of HC in local diversity

Code 
tar_read(correl)

Supporting Figure 7: Correlogram of HC and physical environmental variables

Density of macrofauna

Code 
tar_read(densselR2)
     variables order         R2     R2Cum  AdjR2Cum         F pvalue
1 Current_mean     6 0.17694646 0.1769465 0.1745677 74.385774  0.001
2       Gravel     2 0.04042285 0.2173693 0.2128323 17.819240  0.001
3           OM     3 0.03316824 0.2505375 0.2440015 15.224076  0.001
4    Fetch_max     8 0.05378450 0.3043220 0.2962092 26.518138  0.001
5    PC1_score     9 0.02568327 0.3300053 0.3202101 13.110071  0.001
6       T_mean     4 0.01314023 0.3431455 0.3315880  6.821629  0.012
Code 
tar_load(c(modfixdens12, modfdsel, modrdsel))
jtools::export_summs(
  modfixdens12,
  modfdsel,
  modrdsel,
  model.names = c("Density ~ Complexity", "Density ~ Complexity + Environment", "Density ~ Complexity + Environment + (1|Site)"),
  statistics = c(
    N = "nobs",
    DF = "df.residual",
    AIC = "AIC",
    BIC = "BIC",
    `Marginal R2` = "r.squared.fixed",
    `Conditional R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
    coefs = c(
    "Rhodolith complexity (PC1)" = "PC1_score", 
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "PC1_score:PC2_score",
    "Mean current velocity" = "Current_mean",
    "Depth",
    "Exposure" = "Fetch_max",
    "Gravel",
    "Organic Matter %" = "OM",
    "Mean Temperature" = "T_mean",
    "Year"
  ),
  scale = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 1: Model statistics of macrofaunal density as a function of HC
Density ~ Complexity Density ~ Complexity + Environment Density ~ Complexity + Environment + (1|Site)
Rhodolith complexity (PC1) 0.42 *** (0.05) 0.21 *** (0.06) 0.06    (0.05)
Bed complexity (PC2) 0.09     (0.05) -0.07     (0.05) 0.13    (0.07)
PC1:PC2 -0.31 *** (0.05) -0.14 **  (0.05) 0.04    (0.04)
Mean current velocity              -0.27 *** (0.05) -0.50    (0.24)
Depth              -0.29 *** (0.06) 0.08    (0.14)
Exposure              0.20 **  (0.07) 0.18    (0.18)
Gravel              0.24 *** (0.04) 0.05    (0.05)
Organic Matter %              0.20 *** (0.05) 0.14 ** (0.05)
Mean Temperature              0.11 **  (0.04) 0.06    (0.03)
Year              0.03     (0.04) 0.05    (0.03)
N 348             348             348           
DF 344.00          337.00          335.00        
AIC 889.58          767.68          687.22        
BIC 908.84          813.91          737.30        
Marginal R2                           0.24        
Conditional R2 0.26          0.50          0.69        
Adjusted R2 0.25          0.48                     
F 39.42          33.22                     
p-value 0.00          0.00                     
All continuous predictors are mean-centered and scaled by 1 standard deviation. The outcome variable is in its original units. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_load(c(modfdann, modrdann, modfdart, modrdart, modfdmol, modrdmol, modfdepi, modrdepi, modfdinf, modrdinf, modfdint, modrdint))

jtools::export_summs(
  modfdann,
  modrdann,
  modfdart,
  modrdart,
  modfdmol,
  modrdmol,
  model.names = c("Annelida LM","Annelida LMM", "Arthropoda LM", "Arthropoda LMM", "Mollusca LM", "Mollusca LMM"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `Marginal R2` = "r.squared.fixed",
    `Conditional R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "PC1_score", 
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "PC1_score:PC2_score",
    "Mean current velocity" = "Current_mean",
    "Depth",
    "Exposure" = "Fetch_max",
    "Gravel",
    "Organic Matter %" = "OM",
    "Mean Temperature" = "T_mean",
    "Year"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 2: Model statistics of Density as a function of HC for each main phyla
Annelida LM Annelida LMM Arthropoda LM Arthropoda LMM Mollusca LM Mollusca LMM
Rhodolith complexity (PC1) 0.05     (0.05) 0.07     (0.05) 0.31 *** (0.07) 0.03   (0.05) 0.02     (0.05) -0.02     (0.06)
Bed complexity (PC2) 0.11 *   (0.05) 0.11     (0.07) 0.00     (0.06) 0.10   (0.06) 0.31 *** (0.05) 0.18 **  (0.07)
PC1:PC2 -0.01     (0.04) 0.05     (0.05) -0.18 *** (0.05) 0.06   (0.04) -0.05     (0.04) -0.01     (0.05)
Mean current velocity                           -0.29 *** (0.06) -0.10   (0.22)                          
Depth -0.31 *** (0.05) -0.21 *   (0.10)                         -0.42 *** (0.06) -0.36 *** (0.10)
Exposure -0.29 *** (0.06) -0.37 **  (0.12) 0.30 *** (0.07) 0.31   (0.18)                          
Gravel                           0.31 *** (0.05) 0.02   (0.04) 0.17 *** (0.04) 0.05     (0.05)
Organic Matter % 0.06     (0.05)              0.22 *** (0.06) 0.10 * (0.05) 0.09 *   (0.05) 0.12 *   (0.06)
Mean Temperature 0.09 *   (0.04) 0.07 *   (0.04)                         0.10 **  (0.04) 0.09 *   (0.04)
Year 0.15 *** (0.04) 0.16 *** (0.03) 0.06     (0.04) 0.07 * (0.03) -0.06     (0.04) -0.06     (0.04)
N 348             348             348             348           348             348            
Residual DF 338.00          338.00          339.00          337.00        339.00          337.00         
Marginal R2              0.47                       0.04                     0.35         
Conditional R2 0.59          0.58          0.37          0.75        0.54          0.47         
Adjusted R2 0.58                       0.36                     0.53                      
F 53.91                       24.94                     49.88                      
p-value 0.00                       0.00                     0.00                      
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(anndenspc1)
tar_read(anndenspc2) 
tar_read(artdenspc1)
tar_read(artdenspc2)
tar_read(moldenspc1)
tar_read(moldenspc2)

Main phyla density as a function of HC

Code 
jtools::export_summs(
  modfdepi,
  modrdepi,
  modfdinf,
  modrdinf,
  modfdint,
  modrdint,
  model.names = c("Epifauna LM", "Epifauna LMM", "Infauna LM", "Infauna LMM", "Interstitial fauna LM", "Interstitial fauna LMM"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `Marginal R2` = "r.squared.fixed",
    `Conditional R2` = "r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "PC1_score", 
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "PC1_score:PC2_score",
    "Mean current velocity" = "Current_mean",
    "Depth",
    "Exposure" = "Fetch_max",
    "Gravel",
    "Organic Matter %" = "OM",
    "Mud",
    "Mean Temperature" = "T_mean",
    "Temperature Variation (sd)" = "T_sd",
    "Year"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 3: Model statistics of density of macrofauna as a function of HC for each compartiment
Epifauna LM Epifauna LMM Infauna LM Infauna LMM Interstitial fauna LM Interstitial fauna LMM
Rhodolith complexity (PC1) 0.31 *** (0.06) 0.07    (0.05) 0.10     (0.05) 0.01   (0.06) 0.06     (0.05) 0.04     (0.05)
Bed complexity (PC2) 0.01     (0.05) 0.11    (0.07) 0.17 *** (0.05) 0.14   (0.07) 0.22 *** (0.04) 0.20 **  (0.06)
PC1:PC2 -0.09     (0.05) 0.07    (0.04) -0.11 *   (0.05) -0.00   (0.05) -0.09 *   (0.04) -0.03     (0.05)
Mean current velocity -0.28 *** (0.06) -0.23    (0.21)                                                  
Depth                          -0.48 *** (0.06) -0.20   (0.12)                          
Exposure 0.27 *** (0.07) 0.21    (0.18)                         -0.34 *** (0.06) -0.40 *** (0.09)
Gravel 0.38 *** (0.05) 0.07    (0.05) -0.25 *** (0.05) -0.10   (0.05) 0.26 *** (0.04) 0.19 *** (0.05)
Organic Matter % 0.27 *** (0.05) 0.16 ** (0.05)                         0.03     (0.05) 0.04     (0.05)
Mud                                                  0.33 *** (0.05) 0.25 *** (0.06)
Mean Temperature 0.08     (0.04) 0.04    (0.03) 0.08     (0.04) 0.05   (0.04)                          
Temperature Variation (sd)                          -0.01     (0.04) -0.01   (0.06)                          
Year 0.00     (0.04) 0.02    (0.03) 0.09 *   (0.04) 0.09 * (0.04) 0.14 *** (0.03) 0.14 *** (0.03)
N 348             348            348             348           348             348            
Residual DF 338.00          336.00         339.00          337.00        339.00          337.00         
Marginal R2              0.09                      0.11                     0.56         
Conditional R2 0.42          0.66         0.43          0.49        0.60          0.62         
F 27.06                      32.32                     64.41                      
p-value 0.00                      0.00                     0.00                      
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(epidenspc1)
tar_read(epidenspc2) 
tar_read(infdenspc1)
tar_read(infdenspc2)
tar_read(intdenspc1)
tar_read(intdenspc2)

Density of macrofauna as a function of HC at each compartment

Figure 2  

Code 
tar_read(psdens)
tar_read(psdtrait)

Comparison by Phylum

Comparison by Trait (not added in main text)

Figure 2 (main text)

Observed richness

Check if the relationships between HC and species richness are the same for the total macrofauna as well as for the main phyla and the main compartments (different positions in sediment) separately.

Now we first forward select environmental variables and then add sites as a random factor to control for pseudo-replication and other site-related variables that were not taken into account.

Figure 3  

Code 
tar_read(totrichpc1)
tar_read(figure3)

Bed complexity

Rhodolith complexity

Figure 3. OLS linear regression of Total Macrofauna Richness as a function of HC

Code 
tar_read(richselR2)
  variables order          R2     R2Cum  AdjR2Cum          F pvalue
1     Depth     7 0.329480820 0.3294808 0.3275429 170.018051  0.001
2 Fetch_max     8 0.049649871 0.3791307 0.3755314  27.589068  0.001
3    T_mean     4 0.019017288 0.3981480 0.3928993  10.869694  0.002
4      Year    11 0.008659246 0.4068072 0.3998895   5.007009  0.023
5 PC2_score    10 0.008178651 0.4149859 0.4064330   4.781250  0.033
6 PC1_score     9 0.011702850 0.4266887 0.4166011   6.960742  0.005
7        OM     3 0.008783926 0.4354727 0.4238500   5.290328  0.017
Code 
tar_load(c(modfixrich12, modfrsel, modrrsel))

jtools::export_summs(
  modfixrich12,
  modfrsel,
  modrrsel,
  model.names = c("S ~ Complexity", "S ~ Complexity + Environment", "S ~ Complexity + Environment + (1|Site)"),
  statistics = c(
    N = "nobs",
    DF = "df.residual",
    AIC = "AIC",
    BIC = "BIC",
    `Marginal R2` = "r.squared.fixed",
    `Conditional R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
  coefs = c(
    "Rhodolith complexity (PC1)" = "PC1_score", 
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "PC1_score:PC2_score",
    "Depth",
    "Exposure" = "Fetch_max",
    "Mean bottom temperature" = "T_mean",
    "Organic Matter %" = "OM",
    "Year"
  ),
  scale = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 4: Model statistics of the final selected models of Richness
S ~ Complexity S ~ Complexity + Environment S ~ Complexity + Environment + (1|Site)
Rhodolith complexity (PC1) 8.38 *** (0.91) 2.89 *   (1.20) 2.08    (1.30)
Bed complexity (PC2) 8.03 *** (0.92) 4.30 *** (1.15) 4.05 *  (1.58)
PC1:PC2 -0.87     (0.97) 0.04     (0.91) 2.04    (1.10)
Depth              -5.33 *** (1.25) -3.06    (2.45)
Exposure              -2.75     (1.41) -1.54    (2.83)
Mean bottom temperature              2.05 *   (0.88) 1.38    (0.86)
Organic Matter %              2.56 *   (1.12) 3.72 ** (1.23)
Year              1.71     (0.87) 1.78 *  (0.83)
N 348             348             348           
DF 344.00          339.00          337.00        
AIC 2956.83          2905.35          2872.96        
BIC 2976.10          2943.88          2915.33        
Marginal R2                           0.29        
Conditional R2 0.33          0.44          0.43        
Adjusted R2 0.32          0.42                     
F 55.56          32.69                     
p-value 0.00          0.00                     
All continuous predictors are mean-centered and scaled by 1 standard deviation. The outcome variable is in its original units. *** p < 0.001; ** p < 0.01; * p < 0.05.

You might notice that PC1 was not selected as it has a very small effect size and doesn’t contribute enough to the adjusted R2. I kept it in the final model anyways for comparison with the complexity-only model.

Code 
tar_load(c(modfixrich1, modfixrichpoly1, modfixrich2, modfixrichpoly2, modfixrich12, modfixrichpoly12))

jtools::export_summs(
  modfixrich1, 
  modfixrichpoly1,
  modfixrich2,
  modfixrichpoly2,
  modfixrich12,
  modfixrichpoly12,
  # model.names = c("Linear", "Quadratic"),
  statistics = c(
    N = "nobs",
    DF = "df.residual",
    AIC = "AIC",
    BIC = "BIC",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
  # coefs = c(
  #   "Rhodolith complexity (PC1)" = "PC1_score", 
  #   "Bed complexity (PC2)" = "PC2_score",
  #   "PC1:PC2" = "PC1_score:PC2_score",
  #   "Depth",
  #   "Exposure" = "Fetch_max",
  #   "Mean bottom temperature" = "T_mean",
  #   "Organic Matter %" = "OM",
  #   "Year"
  # ),
  scale = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 5: Model statistics of the linear and unimodal models of Richness
Model 1 Model 2 Model 3 Model 4 Model 5 Model 6
(Intercept) 68.07 *** (1.00) 68.07 *** (1.00) 68.07 *** (1.00) 68.07 *** (1.00) 68.07 *** (0.90) 66.67 *** (0.96)
PC1_score 8.22 *** (1.00)                                        8.38 *** (0.91)             
`poly(PC1_score, 2)`1              8.21 *** (1.00)                                        6.96 *** (1.02)
`poly(PC1_score, 2)`2              1.37     (1.00)                                        -1.25     (1.06)
PC2_score                           8.14 *** (1.00)              8.03 *** (0.92)             
`poly(PC2_score, 2)`1                                        8.14 *** (1.00)              8.89 *** (1.17)
`poly(PC2_score, 2)`2                                        0.44     (1.00)              1.30     (1.20)
PC1_score:PC2_score                                                     -0.87     (0.97)             
`poly(PC1_score, 2)`1:`poly(PC2_score, 2)`1                                                                  1.64     (1.30)
`poly(PC1_score, 2)`2:`poly(PC2_score, 2)`1                                                                  4.02 **  (1.25)
`poly(PC1_score, 2)`1:`poly(PC2_score, 2)`2                                                                  -1.80     (1.30)
`poly(PC1_score, 2)`2:`poly(PC2_score, 2)`2                                                                  -3.58 **  (1.19)
N 348             348             348             348             348             348            
DF 346.00          345.00          346.00          345.00          344.00          339.00         
AIC 3028.54          3028.65          3029.73          3031.53          2956.83          2945.82         
BIC 3040.09          3044.06          3041.28          3046.94          2976.10          2984.35         
Adjusted R2 0.16          0.16          0.16          0.16          0.32          0.35         
F 67.23          34.64          65.82          32.93          55.56          24.45         
p-value 0.00          0.00          0.00          0.00          0.00          0.00         
All continuous predictors are mean-centered and scaled by 1 standard deviation. The outcome variable is in its original units. *** p < 0.001; ** p < 0.01; * p < 0.05.

Figure 4  

Code 
tar_read(psrich)

Figure 4 (main text)
Code 
tar_load(c(modrrann, modrrart, modrrmol, modrrepi, modrrinf, modrrint))

jtools::export_summs(
  modrrann,
  modrrart,
  modrrmol,
  model.names = c("Annelida", "Arthropoda", "Mollusca"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `Marginal R2` = "r.squared.fixed",
    `Conditional R2` = "r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
  coefs = c(
    "Rhodolith complexity (PC1)" = "PC1_score", 
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "PC1_score:PC2_score"
  ),
  scale = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 6: Model statistics of richness as a function of HC for each main phyla
Annelida Arthropoda Mollusca
Rhodolith complexity (PC1) 1.50 *  (0.66) 0.43 (0.44) -0.15 (0.48)
Bed complexity (PC2) 2.50 ** (0.82) 0.90 (0.54) 0.11 (0.60)
PC1:PC2 1.50 ** (0.56) 0.59 (0.36) 0.06 (0.40)
N 348            348         348        
Residual DF 342.00         342.00      342.00     
Marginal R2 0.11         0.02      0.00     
Conditional R2 0.38         0.52      0.51     
p-value                              
All continuous predictors are mean-centered and scaled by 1 standard deviation. The outcome variable is in its original units. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(annrichpc1)
tar_read(annrichpc2) 
tar_read(artrichpc1)
tar_read(artrichpc2)
tar_read(molrichpc1)
tar_read(molrichpc2)

Main phyla richness as a function of HC

Code 
jtools::export_summs(
  modrrepi,
  modrrinf,
  modrrint,
  model.names = c("Epifauna", "Infauna", "Interstitial fauna"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `Marginal R2` = "r.squared.fixed",
    `Conditional R2` = "r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
    coefs = c(
    "Rhodolith complexity (PC1)" = "PC1_score", 
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "PC1_score:PC2_score"
  ),
  scale = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 7: Model statistics of richness as a function of HC for each compartiment
Epifauna Infauna Interstitial fauna
Rhodolith complexity (PC1) 0.78   (0.74) 0.37 (0.56) 0.80 **  (0.29)
Bed complexity (PC2) 1.47   (0.93) 1.35 (0.70) 1.35 *** (0.35)
PC1:PC2 1.40 * (0.62) 0.76 (0.47) 0.36     (0.25)
N 348           348         347            
Residual DF 342.00        342.00      341.00         
Marginal R2 0.03        0.03      0.15         
Conditional R2 0.52        0.44      0.31         
p-value                                 
All continuous predictors are mean-centered and scaled by 1 standard deviation. The outcome variable is in its original units. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(epirichpc1)
tar_read(epirichpc2) 
tar_read(infrichpc1)
tar_read(infrichpc2)
tar_read(intrichpc1)
tar_read(intrichpc2)

Species richness as a function of HC at each faunal compartment

As we can see, the marginal R2 for the models containing only a subset of the macrofauna are quite low. However, although the effects of HC are less evident in these cases, The pattern for most subsets is very similar to the general patter, with very slight positive effect of rhodolith complexity and a more important positive effect of bed complexity. Nevertheless Rhodolith complexity seems to play a more important role in driving annelid richness than the other main phyla.

N2

Code 
tar_read(psN2)

Supporting Figure 8: Regression coefficients of LMs and LMM of Simpson’s inverse diversity (N2) as a function of HC and physical environmental variables.

J

Code 
tar_read(psJ)

Supporting Figure 9: Regression coefficients of LMs and LMM of Pielou’s evenness (J) as a function of HC and physical

Regional patterns of biodiversity

PCA

Code 
tar_read(spfauna)

Screeplot of the PCA of log-chord transformed density data of total macrofauna

Final PCA showing only the species with a godness of fit \(\geq\) .3

Figure 5  

Code 
tar_read(faunapca)

Figure 5 (main text)

Cluster

Code 
tar_read(faunaclust)

Supporting Figure 10: Ward’s cluster of median complexity values at the site level

Effects of HC on regional diversity patterns

Redundancy analysis

After variable selection, we add sites as a factor to understand if we describe them well with the environmental variables we chose. We can look at the first two axes to have an idea of the relationships between the different explanatory variables.

Code 
tar_read(rdafsel)
           variables order          R2     R2Cum   AdjR2Cum         F pvalue
1                Mud     2 0.087006599 0.0870066 0.08436789 32.973166  0.001
2              Depth     8 0.052115736 0.1391223 0.13413174 20.885579  0.001
3       Current_mean     7 0.052409189 0.1915315 0.18448093 22.299894  0.001
4  Branching_density    10 0.037531459 0.2290630 0.22007246 16.698239  0.001
5          Fetch_max     9 0.027419847 0.2564828 0.24561270 12.612470  0.001
6             Gravel     3 0.020457534 0.2769404 0.26421791  9.647916  0.001
7               T_sd     6 0.018777784 0.2957181 0.28121823  9.065187  0.001
8               Year     1 0.012098797 0.3078169 0.29148224  5.925444  0.001
9                  L    11 0.010714212 0.3185312 0.30038554  5.314115  0.001
10               DR3    14 0.010718859 0.3292500 0.30934645  5.385398  0.001
11            T_mean     5 0.008804358 0.3380544 0.31638353  4.469044  0.001
12                OM     4 0.006918997 0.3449734 0.32150973  3.538580  0.001
13        Sphericity    13 0.005596140 0.3505695 0.32529227  2.878077  0.001
14     Total_Density    12 0.003994117 0.3545636 0.32742816  2.060685  0.001
Code 
tar_load(rdasite)
tar_read(triplotrda)

RDA triplot showing the variability in species composition related to physical environmental variables and habitat complexity. The first two axes are shown.
Code 
RsquareAdj(rdasite)$adj.r.squared
[1] 0.4279943

We check the model’s validity. Only 99 permutations were chosen for the validation by axis and by term here as they are really time consuming but the results are the same with 999 permutations. (Output is collapsed, click on code to see)

Code 
tar_read(aovsite)
## Permutation test for rda under reduced model
## Permutation: free
## Number of permutations: 999
## 
## Model: rda(formula = bcdens ~ Mud + Depth + Current_mean + Branching_density + Fetch_max + T_sd + Sphericity + T_mean + DR3 + Gravel + Total_Density + L + OM + Year + Site, data = envcomp)
##           Df Variance      F Pr(>F)    
## Model     23  0.28507 12.289  0.001 ***
## Residual 324  0.32679                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
tar_read(aovaxis)
## Permutation test for rda under reduced model
## Forward tests for axes
## Permutation: free
## Number of permutations: 99
## 
## Model: rda(formula = bcdens ~ Mud + Depth + Current_mean + Branching_density + Fetch_max + T_sd + Sphericity + T_mean + DR3 + Gravel + Total_Density + L + OM + Year + Site, data = envcomp)
##           Df Variance       F Pr(>F)   
## RDA1       1  0.07620 75.5463   0.01 **
## RDA2       1  0.04629 45.8898   0.01 **
## RDA3       1  0.04244 42.0730   0.01 **
## RDA4       1  0.02841 28.1713   0.01 **
## RDA5       1  0.01876 18.5971   0.01 **
## RDA6       1  0.01339 13.2736   0.01 **
## RDA7       1  0.01225 12.1454   0.01 **
## RDA8       1  0.00957  9.4930   0.01 **
## RDA9       1  0.00781  7.7480   0.01 **
## RDA10      1  0.00710  7.0381   0.01 **
## RDA11      1  0.00557  5.5256   0.01 **
## RDA12      1  0.00307  3.0402   0.01 **
## RDA13      1  0.00239  2.3719   0.04 * 
## RDA14      1  0.00202  2.0023   0.12   
## RDA15      1  0.00176  1.7401   0.38   
## RDA16      1  0.00154  1.5284   0.72   
## RDA17      1  0.00133  1.3138   0.96   
## RDA18      1  0.00113  1.1189   1.00   
## RDA19      1  0.00103  1.0169   1.00   
## RDA20      1  0.00088  0.8709   1.00   
## RDA21      1  0.00077  0.7609   1.00   
## RDA22      1  0.00073  0.7236   1.00   
## RDA23      1  0.00065  0.6482   1.00   
## Residual 324  0.32679                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
tar_read(aovterm)
## Permutation test for rda under reduced model
## Terms added sequentially (first to last)
## Permutation: free
## Number of permutations: 99
## 
## Model: rda(formula = bcdens ~ Mud + Depth + Current_mean + Branching_density + Fetch_max + T_sd + Sphericity + T_mean + DR3 + Gravel + Total_Density + L + OM + Year + Site, data = envcomp)
##                    Df Variance       F Pr(>F)   
## Mud                 1  0.05324 52.7815   0.01 **
## Depth               1  0.03189 31.6154   0.01 **
## Current_mean        1  0.03207 31.7934   0.01 **
## Branching_density   1  0.02296 22.7680   0.01 **
## Fetch_max           1  0.01678 16.6339   0.01 **
## T_sd                1  0.01202 11.9166   0.01 **
## Sphericity          1  0.00898  8.9014   0.01 **
## T_mean              1  0.00709  7.0263   0.01 **
## DR3                 1  0.00610  6.0457   0.01 **
## Gravel              1  0.00858  8.5018   0.01 **
## Total_Density       1  0.00236  2.3400   0.01 **
## L                   1  0.00491  4.8632   0.01 **
## OM                  1  0.00426  4.2272   0.01 **
## Year                1  0.00573  5.6773   0.01 **
## Site                9  0.06813  7.5051   0.01 **
## Residual          324  0.32679                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Hierarchical partitioning

Figure 6  

Code 
tar_read(upsetmain)

Figure 6 (main text)
Code 
tar_read(upsetsep)

Hierarchical partitioning separating Rhodolith and Bed complexity

Community stability

Figure 7  

Code 
tar_read(bdplot)

Figure 7 (main text)
Code 
tar_read(replplot)

Supporting Figure 11: Relative importance of the Replacement component of temporal BD

Effects of HC on community stability

Code 
tar_load(c(modbdtot, modrdftot, modrptot))
jtools::export_summs(
  modbdtot,
  modrptot,
  modrdftot,
  model.names = c("BDtotal", "Replacement", "Richness Difference"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "`poly(PC1_score, 2)`1",
    "Rhodolith complexity (PC1)^2" = "`poly(PC1_score, 2)`2",
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "`poly(PC1_score, 2)`1:PC2_score",
    "PC1ˆ2:PC2" = "`poly(PC1_score, 2)`2:PC2_score"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 8: Models statistics of temporal diversity metrics as a function of HC
BDtotal Replacement Richness Difference
Rhodolith complexity (PC1) -0.51 ** (0.16) -0.42 * (0.17) -0.29 (0.18)
Rhodolith complexity (PC1)^2 -0.23    (0.16) -0.10   (0.17) -0.27 (0.19)
Bed complexity (PC2) -0.18    (0.17) -0.21   (0.19) -0.02 (0.20)
PC1:PC2 0.28    (0.19) 0.11   (0.21) 0.32 (0.22)
PC1ˆ2:PC2 -0.07    (0.20) -0.27   (0.22) 0.24 (0.24)
N 30            30           30        
Residual DF 24.00         24.00        24.00     
R2 0.43         0.32        0.20     
Adjusted R2 0.31         0.18        0.03     
F 3.55         2.23        1.20     
p-value 0.02         0.08        0.34     
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(bdtotpc1)
tar_read(bdtotpc2)
tar_read(rdtotpc1)
tar_read(rdtotpc2)
tar_read(rptotpc1)
tar_read(rptotpc2)

Effects of HC on community stability

Effects of HC on community stability

Effects of HC on community stability

Effects of HC on community stability

Effects of HC on community stability

Effects of HC on community stability
Code 
tar_load(c(modbdann, modrdfann, modrpann))
jtools::export_summs(
  modbdann,
  modrpann,
  modrdfann,
  model.names = c("BDtotal", "Replacement", "Richness Difference"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "`poly(PC1_score, 2)`1",
    "Rhodolith complexity (PC1)^2" = "`poly(PC1_score, 2)`2",
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "`poly(PC1_score, 2)`1:PC2_score",
    "PC1ˆ2:PC2" = "`poly(PC1_score, 2)`2:PC2_score"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 9: Models statistics of annelid temporal diversity metrics as a function of HC
BDtotal Replacement Richness Difference
Rhodolith complexity (PC1) -0.61 *** (0.14) -0.64 *** (0.15) -0.16 (0.19)
Rhodolith complexity (PC1)^2 -0.27     (0.15) -0.11     (0.15) -0.30 (0.19)
Bed complexity (PC2) -0.08     (0.16) 0.01     (0.16) -0.14 (0.20)
PC1:PC2 0.22     (0.17) 0.10     (0.18) 0.22 (0.23)
PC1ˆ2:PC2 -0.10     (0.19) -0.22     (0.19) 0.12 (0.24)
N 30             30             30        
Residual DF 24.00          24.00          24.00     
R2 0.51          0.49          0.18     
Adjusted R2 0.41          0.38          0.01     
F 4.98          4.62          1.03     
p-value 0.00          0.00          0.42     
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(bdannpc1)
tar_read(bdannpc2)
tar_read(rdannpc1)
tar_read(rdannpc2)
tar_read(rpannpc1)
tar_read(rpannpc2)

Effects of HC on annelid community stability

Effects of HC on annelid community stability

Effects of HC on annelid community stability

Effects of HC on annelid community stability

Effects of HC on annelid community stability

Effects of HC on annelid community stability
Code 
tar_load(c(modbdart, modrdfart, modrpart))
jtools::export_summs(
  modbdart,
  modrpart,
  modrdfart,
  model.names = c("BDtotal", "Replacement", "Richness Difference"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "`poly(PC1_score, 2)`1",
    "Rhodolith complexity (PC1)^2" = "`poly(PC1_score, 2)`2",
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "`poly(PC1_score, 2)`1:PC2_score",
    "PC1ˆ2:PC2" = "`poly(PC1_score, 2)`2:PC2_score"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 10: Models statistics of arthropod temporal diversity metrics as a function of HC
BDtotal Replacement Richness Difference
Rhodolith complexity (PC1) -0.42 * (0.17) -0.29   (0.16) -0.38 * (0.18)
Rhodolith complexity (PC1)^2 -0.09   (0.18) -0.20   (0.16) 0.03   (0.18)
Bed complexity (PC2) -0.23   (0.19) -0.40 * (0.18) -0.02   (0.20)
PC1:PC2 0.22   (0.21) -0.13   (0.19) 0.41   (0.22)
PC1ˆ2:PC2 -0.11   (0.22) -0.41   (0.21) 0.16   (0.23)
N 30           30           30          
Residual DF 24.00        24.00        24.00       
R2 0.31        0.39        0.25       
Adjusted R2 0.16        0.27        0.09       
F 2.14        3.11        1.57       
p-value 0.10        0.03        0.21       
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(bdartpc1)
tar_read(bdartpc2)
tar_read(rdartpc1)
tar_read(rdartpc2)
tar_read(rpartpc1)
tar_read(rpartpc2)

Effects of HC on arthropod community stability

Effects of HC on arthropod community stability

Effects of HC on arthropod community stability

Effects of HC on arthropod community stability

Effects of HC on arthropod community stability

Effects of HC on arthropod community stability
Code 
tar_load(c(modbdmol, modrdfmol, modrpmol))
jtools::export_summs(
  modbdmol,
  modrpmol,
  modrdfmol,
  model.names = c("BDtotal", "Replacement", "Richness Difference"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "`poly(PC1_score, 2)`1",
    "Rhodolith complexity (PC1)^2" = "`poly(PC1_score, 2)`2",
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "`poly(PC1_score, 2)`1:PC2_score",
    "PC1ˆ2:PC2" = "`poly(PC1_score, 2)`2:PC2_score"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 11: Models statistics of mollusc temporal diversity metrics as a function of HC
BDtotal Replacement Richness Difference
Rhodolith complexity (PC1) -0.22 (0.16) -0.06 (0.19) -0.24 (0.18)
Rhodolith complexity (PC1)^2 -0.32 (0.16) -0.16 (0.20) -0.23 (0.19)
Bed complexity (PC2) -0.35 (0.17) -0.22 (0.21) -0.20 (0.20)
PC1:PC2 0.30 (0.19) 0.19 (0.23) 0.15 (0.22)
PC1ˆ2:PC2 0.15 (0.21) 0.02 (0.25) 0.20 (0.24)
N 30         30         30        
Residual DF 24.00      24.00      24.00     
R2 0.40      0.13      0.19     
Adjusted R2 0.27      -0.05      0.03     
F 3.18      0.72      1.16     
p-value 0.02      0.62      0.36     
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(bdmolpc1)
tar_read(bdmolpc2)
tar_read(rdmolpc1)
tar_read(rdmolpc2)
tar_read(rpmolpc1)
tar_read(rpmolpc2)

Effects of HC on mollusc community stability

Effects of HC on mollusc community stability

Effects of HC on mollusc community stability

Effects of HC on mollusc community stability

Effects of HC on mollusc community stability

Effects of HC on mollusc community stability
Code 
tar_load(c(modbdepi, modrdfepi, modrpepi))
jtools::export_summs(
  modbdepi,
  modrpepi,
  modrdfepi,
  model.names = c("BDtotal", "Replacement", "Richness Difference"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "`poly(PC1_score, 2)`1",
    "Rhodolith complexity (PC1)^2" = "`poly(PC1_score, 2)`2",
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "`poly(PC1_score, 2)`1:PC2_score",
    "PC1ˆ2:PC2" = "`poly(PC1_score, 2)`2:PC2_score"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 12: Models statistics of epifaunal temporal diversity metrics as a function of HC
BDtotal Replacement Richness Difference
Rhodolith complexity (PC1) -0.42 * (0.18) -0.25 (0.19) -0.38 * (0.18)
Rhodolith complexity (PC1)^2 -0.16   (0.18) -0.06 (0.19) -0.19   (0.19)
Bed complexity (PC2) -0.04   (0.19) -0.07 (0.21) 0.02   (0.20)
PC1:PC2 0.29   (0.21) 0.08 (0.23) 0.36   (0.22)
PC1ˆ2:PC2 -0.05   (0.23) -0.26 (0.25) 0.18   (0.24)
N 30           30         30          
Residual DF 24.00        24.00      24.00       
R2 0.27        0.15      0.22       
Adjusted R2 0.12        -0.03      0.06       
F 1.82        0.82      1.38       
p-value 0.15        0.55      0.27       
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(bdepipc1)
tar_read(bdepipc2)
tar_read(rdepipc1)
tar_read(rdepipc2)
tar_read(rpepipc1)
tar_read(rpepipc2)

Effects of HC on epifaunal community stability

Effects of HC on epifaunal community stability

Effects of HC on epifaunal community stability

Effects of HC on epifaunal community stability

Effects of HC on epifaunal community stability

Effects of HC on epifaunal community stability
Code 
tar_load(c(modbdinf, modrdfinf, modrpinf))
jtools::export_summs(
  modbdinf,
  modrpinf,
  modrdfinf,
  model.names = c("BDtotal", "Replacement", "Richness Difference"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "`poly(PC1_score, 2)`1",
    "Rhodolith complexity (PC1)^2" = "`poly(PC1_score, 2)`2",
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "`poly(PC1_score, 2)`1:PC2_score",
    "PC1ˆ2:PC2" = "`poly(PC1_score, 2)`2:PC2_score"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 13: Models statistics of infaunal temporal diversity metrics as a function of HC
BDtotal Replacement Richness Difference
Rhodolith complexity (PC1) -0.56 *** (0.14) -0.43 * (0.17) -0.28 (0.18)
Rhodolith complexity (PC1)^2 -0.35 *   (0.14) -0.25   (0.17) -0.20 (0.19)
Bed complexity (PC2) -0.26     (0.15) -0.16   (0.18) -0.19 (0.20)
PC1:PC2 0.18     (0.16) 0.09   (0.20) 0.17 (0.22)
PC1ˆ2:PC2 -0.09     (0.18) -0.18   (0.22) 0.13 (0.24)
N 30             30           30        
Residual DF 24.00          24.00        24.00     
R2 0.57          0.33        0.19     
Adjusted R2 0.48          0.20        0.03     
F 6.30          2.41        1.15     
p-value 0.00          0.07        0.36     
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(bdinfpc1)
tar_read(bdinfpc2)
tar_read(rdinfpc1)
tar_read(rdinfpc2)
tar_read(rpinfpc1)
tar_read(rpinfpc2)

Effects of HC on infaunal community stability

Effects of HC on infaunal community stability

Effects of HC on infaunal community stability

Effects of HC on infaunal community stability

Effects of HC on infaunal community stability

Effects of HC on infaunal community stability
Code 
tar_load(c(modbdint, modrdfint, modrpint))
jtools::export_summs(
  modbdint,
  modrpint,
  modrdfint,
  model.names = c("BDtotal", "Replacement", "Richness Difference"),
  statistics = c(
    N = "nobs",
    `Residual DF` = "df.residual",
    `R2` = "r.squared",
    `Adjusted R2` = "adj.r.squared",
    `F` = "statistic",
    `p-value` = "p.value"
  ),
   coefs = c(
    "Rhodolith complexity (PC1)" = "`poly(PC1_score, 2)`1",
    "Rhodolith complexity (PC1)^2" = "`poly(PC1_score, 2)`2",
    "Bed complexity (PC2)" = "PC2_score",
    "PC1:PC2" = "`poly(PC1_score, 2)`1:PC2_score",
    "PC1ˆ2:PC2" = "`poly(PC1_score, 2)`2:PC2_score"
  ),
  scale = TRUE,
  transform.response = TRUE,
  error_pos = "right",
  bold_signif = .05
)
Supporting Table 14: Models statistics of interstitial fauna temporal diversity metrics as a function of HC
BDtotal Replacement Richness Difference
Rhodolith complexity (PC1) -0.33   (0.16) -0.46 * (0.17) 0.12 (0.18)
Rhodolith complexity (PC1)^2 -0.12   (0.17) 0.17   (0.17) -0.31 (0.18)
Bed complexity (PC2) -0.40 * (0.18) -0.26   (0.18) -0.16 (0.20)
PC1:PC2 0.26   (0.20) 0.01   (0.20) 0.27 (0.22)
PC1ˆ2:PC2 -0.02   (0.21) -0.32   (0.22) 0.30 (0.23)
N 30           30           30        
Residual DF 24.00        24.00        24.00     
R2 0.38        0.35        0.25     
Adjusted R2 0.25        0.21        0.09     
F 2.92        2.55        1.57     
p-value 0.03        0.05        0.21     
All continuous variables are mean-centered and scaled by 1 standard deviation. *** p < 0.001; ** p < 0.01; * p < 0.05.
Code 
tar_read(bdintpc1)
tar_read(bdintpc2)
tar_read(rdintpc1)
tar_read(rdintpc2)
tar_read(rpintpc1)
tar_read(rpintpc2)

Effects of HC on intersitial community stability

Effects of HC on intersitial community stability

Effects of HC on intersitial community stability

Effects of HC on intersitial community stability

Effects of HC on intersitial community stability

Effects of HC on intersitial community stability

Figure 8  

Code 
tar_read(bdtrait)
tar_read(bdphyl)

Effects of HC on community stability by compartiment

Effects of HC on community stability by phylum - not shown in main text

Figure 8 (main text)

References

Box, G. E. P., and D. R. Cox. 1964. “An Analysis of Transformations.” Journal of the Royal Statistical Society. Series B (Methodological) 26 (2): 211–52. https://www.jstor.org/stable/2984418.
Casajus N. 2022. Rcompendium: An r Package to Create a Package or Research Compendium Structure. https://github.com/FRBCesab/rcompendium.
Landau, William Michael. 2021. “The Targets r Package: A Dynamic Make-Like Function-Oriented Pipeline Toolkit for Reproducibility and High-Performance Computing.” Journal of Open Source Software 6 (57): 2959. https://doi.org/10.21105/joss.02959.